Visual Molecular Dynamics

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. It was developed and is maintained by the Theoretical and Computational Biophysics Group of the University of Illinois at Urbana-Champaign (http://www.ks.uiuc.edu)

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

VMD uses OpenGL to provide high performance 3-D molecular graphics The program has many features, which include:

  • No limits on the number of molecules, atoms, residues or number of animation frames, except available memory.
  • Many molecular rendering and coloring methods.
  • Stereo display capability.
  • Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more).
  • Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files.
  • Ability to export displayed graphics to files which may be processed by a number of popular ray tracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
  • Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities.
  • Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis
  • Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code
  • Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical and Computational Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd
  • VMD works well with projected display systems like the 3-D Projection Facility maintained by the Theoretical and Computational Biophysics Group.
  • VMD can be used to concurrently display and interact with a running MD simulation using NAMD.

Hompage: http://www.ks.uiuc.edu/Research/vmd

Usage:

VMD is located in the directory /opt/pc2/VMD and can be started from this directory by typing ./bin/vmd. A detailed PDF documentation can be found in ./lib/vmd/doc/ug.pdf.

It is also possible to run VMD in 3D mode to use it on the steroscopic display wall. This requires some setup and ressource allocation effort. If you want to use this feature or if you have other questions or suggestions please feel free to contact us.

Contact: Jens Simon

HPC Systems & Services